Three-dimensional structures, dynamics and calcium-mediated interactions of the exopolysaccharide, Infernan, produced by the deep-sea hydrothermal bacterium Alteromonas infernus

Type Article
Date 2022-01
Language English
Author(s) Makshakova Olga1, Zykwinska AgataORCID2, Cuenot Stéphane3, Colliec-Jouault SylviaORCID2, Perez Serge4
Affiliation(s) 1 : Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, 420111 Kazan, Russian Federation
2 : Ifremer, Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies, 44311 Nantes, France
3 : Université de Nantes, CNRS, Institut des Matériaux Jean Rouxel, IMN, Nantes, France
4 : Centre de Recherches sur les Macromolécules Végétales, Université de Grenoble Alpes, Centre National de la Recherche Scientifique, Grenoble, France
Source Carbohydrate Polymers (0144-8617) (Elsevier BV), 2022-01 , Vol. 276 , P. 118732 (11p.)
DOI 10.1016/j.carbpol.2021.118732
WOS© Times Cited 7
Keyword(s) Exopolysaccharides, Alteromonas infernus, 3 dimensional structures, Gel forming, Molecular dynamics, Quantum chemistry, Calcium binding
Abstract

The exopolysaccharide Infernan, from the bacterial strain GY785, has a complex repeating unit of nine monosaccharides established on a double-layer of sidechains. A cluster of uronic and sulfated monosaccharides confers to Infernan functional and biological activities. We characterized the 3-dimensional structures and dynamics along Molecular Dynamics trajectories and clustered the conformations in extended two-fold and five-fold helical structures. The electrostatic potential distribution over all the structures revealed negatively charged cavities explored for Ca2+ binding through quantum chemistry computation. The transposition of the model of Ca2+complexation indicates that the five-fold helices are the most favourable for interactions. The ribbon-like shape of two-fold helices brings neighbouring chains in proximity without steric clashes. The cavity chelating the Ca2+ of one chain is completed throughout the interaction of a sulfate group from the neighbouring chain. The resulting is a ‘junction zone’ based on unique chain-chain interactions governed by a heterotypic binding mode.

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Makshakova Olga, Zykwinska Agata, Cuenot Stéphane, Colliec-Jouault Sylvia, Perez Serge (2022). Three-dimensional structures, dynamics and calcium-mediated interactions of the exopolysaccharide, Infernan, produced by the deep-sea hydrothermal bacterium Alteromonas infernus. Carbohydrate Polymers, 276, 118732 (11p.). Publisher's official version : https://doi.org/10.1016/j.carbpol.2021.118732 , Open Access version : https://archimer.ifremer.fr/doc/00730/84248/